H7N9 low pathogenic influenza viruses emerged in China in 2013 and mutated to highly pathogenic strains in 2017, resulting in human infections and disease in chickens. To control spread, a bivalent H5/H7 inactivated vaccine was introduced in poultry in September 2017. To monitor virus evolution and vaccine efficacy, we collected 53,884 poultry samples across China from February 2017 to January 2018. We isolated 252 H7N9 low pathogenic viruses, 69 H7N9 highly pathogenic viruses, and one H7N2 highly pathogenic virus, of which two low pathogenic and 14 highly pathogenic strains were collected after vaccine introduction. Genetic analysis of highly pathogenic strains revealed nine genotypes, one of which is predominant and widespread and contains strains exhibiting high virulence in mice. Additionally, some H7N9 and H7N2 viruses carrying duck virus genes are lethal in ducks. Thus, although vaccination reduced H7N9 infections, the increased virulence and expanded host range to ducks pose new challenges. Display omitted •In 2017 across China, H7N9 HPAI viruses evolved into different genotypes•H7N9 and H7N2 HPAI reassortants are well adapted and lethal in ducks•An H5/H7 vaccine induced solid protection against H7 viruses in poultry H7N9 highly pathogenic avian influenza viruses emerged in China in 2017, prompting vaccination in poultry. Shi et al. examine H7N9 viruses across China before and after vaccination, revealing rapid evolution into subtypes and genotypes. Although vaccination reduced infections, some H7N9 and H7N2 viruses exhibit heightened virulence and expansion to ducks.